“Anti-terror chief to oversee Muslim schools infiltration claims”, reads the headline about Michael Gove’s appointment of a special commissioner to investigate allegations of a co-ordinated extremist takeover of some Birmingham schools. At first sight, it’s quite shocking – as no doubt the headline writer intended it to be. How could a policeman who used to fight terrorists be better suited to this job than someone from the educational establishment?

Once you start digging down into the story, though, it emerges that Gove has simply made a more accurate assessment of the issues at hand than most. The “Trojan Horse” plot which is alleged isn’t a question of educational standards or headteacher skill-sets, it’s claimed to be a matter of Islamist ideology and the attempted radicalisation of the young. Few people understand better the methods and motivations used in radicalising the young than those who have worked on counter-extremism in recent years – which is why Peter Clarke is a good fit for the task at hand.

The announcement could have been handled better, of course. With such a fraught environment of claim and counter claim in Birmingham at the moment, it would perhaps have been better to explain the choice of commissioner at some length rather than allow the rumour mill (or, if there is a plot, the targets of the investigation) to stir up scare stories about it. The Education Secretary could hardly have expected the local Chief Constable to join in, but perhaps some judicious pre-briefing might have helped to head it off.

Peter Clarke has a big, risky job on his hands. He is plunging into a complex mix of educational standards, religious freedom, alleged extremism, political ideology and localist practice – all under the eyes of the national media. Already, some of Gove’s barrel-scraping opponents are trying to claim the allegations prove that all schools should be run directly by bureaucrats, and local Labour politicians are accusing him of inflaming tensions in Birmingham.

It’s nonsense to use this story to smear the principle of localism. For a start, Birmingham is anything but a localist city – as Fraser Nelson recently noted, while Manchester has devolved power down to smaller councils, Brum’s politicians have jealously clung on to centralised power over a huge population, to ruinous effect. Sir Albert Bore has used the scandal to imply that his authority should control schools that are currently academies – despite the disastrous record in the schools it does run, and horrendous failures in other services such as child protection.

Before the allegations at hand disappear into a wider fog of political war, we should note that they are extremely serious and must be dealt with, regardless of the wider politics. It is claimed that headteachers and other staff who are deemed obstructive are driven out, and schools then shift to a policy and curriculum in keeping with hard-line interpretations of Islam. The allegations include instances of classroom segregation by gender, bans on sex education and even an instance of praise for an extremist preacher.

For some years there has been a campaign for a hard-line interpretation of Islam to be brought into British classrooms. A 2007 education report by the Muslim Council of Britain (no longer on the MCB website, but available here) presented British Muslims as holding a strict interpretation of Islamic teachings, including the concept of hijab being obligatory for all girls, concerns about dancing and opposition to “un-Islamic” music. The foreword to the report was written by one Tahir Alam, who coincidentally is Chairman of Governors at Park View School, Birmingham, and who has expressed outrage that his school is being investigated as part of the response to the Trojan Horse allegations.

Of course, the letter which kicked all this off may turn out to be a hoax, designed to stir up trouble. On the other hand, it may turn out to be accurate. Or the truth could be somewhere in between.

Ultimately, the question will come down to what localism means – do the academy and free school reforms mean the Islamicisation of education is acceptable? Is the new system strong enough to localise while protecting against the type of takeover which is alleged?

Michael Gove argues that there is a difference between the freedom to set school policy and the out and out introduction of “extremist” practices. On the one hand, he does not want to endanger the freedoms of faith schools – on the other, he rightly opposes the infiltration of the education system by those who want to turn schools away from education and towards indoctrination.

It’s a balance that must be struck, lest his opponents use the issue to promote the worst of all worlds – the return of school control to the bureaucrats who gutted the system in the first place.